"Core" Classes like fighter, rogue, cleric, and wizard are hard to spice up in later levels.
Fighters continue getting feats, which are customizable special powers - the only problem is there weren't enough high level feats to stay a fighter, afterall, 4 levels of fighter allow you to get all the same feats a fighter can get (allowing for equivelant BAB). In 3.5 this was remedied to some extent, fighters have more fighter-only feats, although again, after level 12 there is little reason to stick around (unless you want more feats!).
Rogues had a built in mechanic, "Special Ability" which allowed them greater diversity. IMO, this mechanic should have also been used for other classes, like the paladin, who tend to peter out after 10th level. The only problem is most roguish Prcs took it upon themselves to give the core class Rogue's Special Abilities AND other nifty stuff, but if you didn't use prcs which emulat the rogue's special ability list, single class rogues would be quite viable.
Clerics gain spell levels every 2 levels. Inherently, to me, this means that any cleric prc which narrows the focus of the cleric should also narrow spellcasting. Restrict a school of spells, take away bonus domain spells, or reduce the cleric's combat effectiveness (BAB + HD) if you want to give them full spellcasting AND nifty abilities. Unfortunately, this is not the way it is usually handled, so clerics (which are a strong class anyway) get even more buff and don't "lose out" on any abilities (except turn undead and possibly domain powers) for gaining a prc.
Wizards are in the same boat as clerics, except they don't have combat effectiveness to give up. So the only way to narrow the focus is to restrict spellcasting in some way. Ban schools of spells, reduce caster level, don't give out spellcasting at every level - something must be done to make a proper wizard prc, else a wizard only misses a couple bonus feats and some familiar progression for leaving Wizard.
I think 3.5 tried to remedy the problem with the non-core classes. Take a look at the 3.5 barbarian for instance, he's set up more like the monk with constant abilities all the way up to 20. While most enhance his rage in some ways, going to a prc means his rage will be less effective, and he will probably have less DR than a regular barbarian. This is also true of the ranger, who misses out on some nifty things like HiPS or Camoflauge by multiclassing. I think the paladin still needs a better reason to stick around besides "powering up" paladin abilities (see above). The bard was also "fixed" for multiclassing, by allowing increasingly better songs and songs getting powered up at higher levels.
The sorceror is basically the same as the wizard argument above, with the caveat that since they can't learn all the spells they want anyway, its more difficult to restrict them even further in spell selection. The druid has never really had a problem, since going to a prc means missing out on wildshape abilities, but this is punctuated even more in 3.5 with Tree Shape and slightly more elemental shaping at higher levels (not to mention things like no more aging or alter self at will).
Overall, I think its difficult to continue giving "core" classes bennies every level, a core class (imo) is best suited by allowing a lot of flexibility and generality. A prc is suited by narrowing a core class's focus. A non-core class (barb, ranger, etc) is suited by having abilities that scale as they level and higher level abilities which make it a harder decision to get prc levels.
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